Mutation rates

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In genetics, the mutation rate is a measure of the rate at which various types of mutations occur during some unit of time. Mutation rates are typically given for a specific class of mutation, for instance point mutations, small or large scale insertions or deletions. The rate of substitutions can be further subdivided into a mutation spectrum which describes the influence of genetic context on the mutation rate.

Resources

Y-chromosome STR mutation rates. A downloadable spreadsheet provided by Tim Janzen showing comparative mutation rates for 113 Y-STR markers. The data has been compiled from a number of sources (John Chandler, Doug McDonald, Charles Kerchner, SMGF, Ysearch, YHRD, Marko Heinila, Chris Rottensteiner and from the peer-reviewed literature).
A table of mutation rates for 111 markers provided by Marko Heinila in collaboration with Iain McDonald
List of DYS markers and associated mutation rates from Wikipedia
Mutation rates for the markers in the YHRD.org database
Leo Little's chart of mutation rate effects The charts show the percentage of descendant haplotypes with at least 1 mutation after x years
Top 50 mtDNA mutations from the Sorenson Molecular Genealogy Foundation (preserved in the Wayback Machine)
Y-STR database A database of mutation rates of Y-STR markers using results from many studies compiled by the Hawgood DNA project
Charles Kerchner's Y-STR Haplotype Observed Mutation Rates in Surname Projects Study and Log

Blog posts

DNA dating: How molecular clocks are refining human evolution’s timeline by Bridget Alex and Priya Moorjani, The Conversation, 7 April 2017.
Explainer: what is the molecular clock? by Al Tanner, The Conversation, 15 September 2015.
Human Y chromosome mutation rates by Larry Moran, Sandwalk blog, 1 September 2009.

Scientific papers

General articles

Scally A (2106). Mutation rates and the evolution of germline structure. Preprint published online at BioRxiv on 16 May 2016.
James X Sun, Agnar Helgason, Gisli Masson, Sigríður Sunna Ebenesersdóttir, Heng Li, Swapan Mallick, Sante Gnerre, Nick Patterson, Augustine Kong, David Reich & Kari Stefansson (2012). A direct characterization of human mutation based on microsatellites. Letter. Nature Genetics, 23 August 2012.
Callaway, Ewen (2012). Fathers bequeath more mutations as they age. News article. Nature 488, 439 (23 August 2012).

Reviews

Ségurel L, Wyman MJ, Przeworski M (2014). Determinants of mutation rate variation in the human germline. Genomics and Human Genetics 15: 47-70.

Articles on mutation rates in the Y-chromosome

Claerhout S, Vanpaemel S, Gill MS, Antiga LG, Baele G, Decorte R (2021). YMrCA: improving Y-chromosomal ancestor time estimation for DNA kinship research. Human Mutation, published online 15 July 2021.
McDonald I (2021). Improved models of coalescence ages of Y-DNA haplogroups. Genes 12(6), 862.
Ding Q, Hu Y, Koren A, Clark AG. Mutation rate variability across human Y-chromosome haplogroups. Molecular Biology and Evolution 2021; 38 (3): 1000–1005.
Boattini A, Sarno S, Mazzarisi AM et al (2019). Estimating Y-Str mutation rates and Tmrca through deep-rooting Italian pedigrees. Scientific Reports 9: 9032.
Balanovsky O (2017). Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. Human Genetics, published online 28 April 2017. Review article.
Alessio Boattini A. Sarno S, Bini C et al (2016). Mutation rates and discriminating power for 13 rapidly-mutating Y-STRS between related and unrelated individuals. PLOS One. Published 1 November 2016.
Willems T, Gymrek M, Poznik GD, Tyler-Smith S, The 1000 Genomes Project Y-Chromosome Working Group, Erlich Y. Population-scale sequencing data enable precise estimates of Y-STR mutation rates. American Journal of Human Genetics, published online 25 April 2016. Preprint available here.
Trombetta B, D'Atanasio E, Massaia A et al. Regional differences in the accumulation of SNPs on the male-specific portion of the human Y chromosome replicate autosomal patterns: implications for genetic dating. PLOS One Published online: 30 July 2015.
Helgason A, Einarsson AW, Valdís B Guðmundsdóttir VB et al (2015). The Y-chromosome point mutation rate in humans (letter). Nature Genetics, published online 25 March 2015.
Adamov D, Guryanov V, Karzhavin S, Tagankin V, Urasin V. Defining a new rate constant for Y-chromosome SNPs based on full sequencing data. Russian Journal of Genetic Genealogy 2015; 7(1).
Ballantyne KN et al (2014). Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Human Mutation 2014; 35: 1021–1032.
Chuan-Chao Wang C-C. Gilbert MT, Jin L, Li H (2014). Evaluating the Y chromosomal timescale in human demographic and lineage dating [review]. Investigative Genetics 2014; 5: 12.
Wei W, Ayub Q, Xue Y, Tyler-Smith C (2013). A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping. Forensic Science International Genetics 2013 Dec;7 (6): 568-72.
Poznik GD, Henn BM, Yee MC et al (2013). Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 2013 Aug 2; 341(6145):562-5.
- For a critique of this paper and the misconceptions behind it see the three-part series of articles by Melissa Wilson Ayres: Y and mtDNA are not Adam and Eve: Part 1; Y and mtDNA are not Adam and Eve: Part 2 - What it means to be the Most Recent Common Ancestor and Y and mtDNA are not Adam and Eve: Part 3 - Resolving a discrepancy.
Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, Carbone I, Xue Y, Tyler-Smith C (2013). A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Research 2013 Feb; 23(2):388-95.
Concetta Burgarella and Miguel Navascués (2011). Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data. European Journal of Human Genetics 2011; 19, 70–75. Published online 8 September 2010.
Xue, Y. and Tyler-Smith, C (2009). The hare and the tortoise: One small step for four SNPs, one giant leap for SNP-kind. Forensic Science International: Genetics 4(2):59-61.
Yali Xue, Qiuju Wang, Quan Long et al (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Current Biology 2009 September 15; 19(17): 1453–1457.
Anatole A. Klyosov (2009). DNA Genealogy, Mutation Rates, and Some Historical Evidence Written in Y-Chromosome, Part II: Walking the Map Journal of Genetic Genealogy Fall 2009, Volume 5, Number 2.
Eckert KA, Hile SE (2009). Every microsatellite is different: Intrinsic DNA features dictate mutagenesis of common microsatellites present in the human genome. Molecular Carcinogenesis. 2009 Apr; 48(4): 379-88.
Anatole Klyosov (2009). DNA Genealogy, Mutation Rates, and Some Historical Evidence Written in Y-Chromosome, Part I: Basic Principles and the Method Journal of Genetic Genealogy Fall 2009, Volume 5, Number 2.
Whit Athey (2007). Mutation Rates – Who’s Got the Right Values? (editorial) Journal of Genetic Genealogy Volume 3, Number 2, Fall/autumn 2007.
John Chandler (2006). Estimating per-locus mutation rates. Journal of Genetic Genealogy, Volume 2, Number 2, Fall/autumn 2006.
Soares PA, Pereira F, Brion M (2005). Relative Y-STR mutation rates estimated from the variance inside SNP defined lineages International Congress Series 1288 (2006) 82–84. Progress in Forensic Genetics 11 — Proceedings of the 21st International ISFG Congress held in Ponta Delgada, The Azores, Portugal between 13 and 16 September 2005.
Budowle B, Adamowicz M, Aranda XG et al (2005). Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Science International 2005 May 28; 150(1): 1-15.
Luke A. D. Hutchison, Natalie M. Myres, Jacob E. Ekins et al, Sorenson Molecular Genealogy Foundation (2004). Direct determination of mutation characteristics of Y chromosome STR loci Presented at the American Society of Human Genetics 2004 Annual Meeting, October 2004, Toronto, Ontario, Canada.
Ellegren H (2004). Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics 5: 435-445. A useful review article providing an overview of mutations occur.
Zhivotovsky LA, Peter A. Underhill PA, Cinnioğlu C et al (2004). The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. American Journal of Human Genetics 2004 January; 74(1): 50–61.
Dupuy B. Myhre, Stenersen M, Egeland T, Olaisen B (2003). Y-chromosomal microsatellite mutation rates: Differences in mutation rate between and within loci. Human Mutation 2003 23 (2): 117-124.
Ulrike Holtkemper, Burkhard Rolf, Carsten Hohoff et al (2001). Mutation rates at two human Y-chromosomal microsatellite loci using small pool PCR techniques. Human Molecular Genetics 2001; 10 (6): 629-633.

Father-son studies

Concetta Burgarella and Miguel Navascués (2011). Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data. European Journal of Human Genetics 2011; 19: 70–75.
Kaye N. Ballantyne, Miriam Goedbloed, Rixun Fang et al (2010). Mutability of Y-Chromosomal Microsatellites: Rates, Characteristics, Molecular Bases, and Forensic Implications. American Journal of Human Genetics Volume 87, Issue 3, 10 September 2010: 341-353.
Ge J, Budowle B, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R (2009). Mutation rates at Y chromosome short tandem repeats in Texas populations. Forensic Science International: Genetics. 2009 Jun;3(3):179-84.
Decker AE, Kline MC, Redman JW, Reid TM, Butler JM (2008). Analysis of mutations in father–son pairs with 17 Y-STR loci. 'Forensic Science International: Genetics 2 2008: e31–e35
Gusmão L, Sánchez-Diz P, Calafell F et al (2005). Mutation rates at Y chromosome specific microsatellites. Human Mutation 2005 Dec; 26(6): 520-528.
Manfred Kayser, Lutz Roewer, Minttu Hedman et al (2000). Characteristics and Frequency of Germline Mutations at Microsatellite Loci from the Human Y Chromosome, as Revealed by Direct Observation in Father/Son Pair. American Journal of Human Genetics 2000; 66: 1580–1588.

Articles on mutation rates in mtDNA

Översti S, Palo JU (2022). Variation in the substitution rates among the human mitochondrial haplogroup U sublineages. Genome Biology and Evolution 14 (7), July 2022, evac097.
Kivisild T (2015). Maternal ancestry and population history from whole mitochondrial genomes. ‘’Investigative Genetics’’ 6: 3.
Rieux A, Eriksson A, Li M et (2014). Improved calibration of the human mitochondrial clock using ancient genomes. Molecular Biology and Evolution 31 (10): 2780–2792.
Fu Q, Mittnik A, Johnson PLF et al (2013). A revised timescale for human evolution based on mitochondrial genomes. Current Biology 2013; 23 (7): 553–559.
Behar DM, Van Oven M, Rosset S (2012). A “Copernican” reassessment of the human mitochondrial DNA tree from its root. American Journal of Human Genetics 2012 Apr 6; 90(4): 675-684.
Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB (2009). Correcting for purifying selection: an improved human mitochondrial molecular clock. American Journal of Human Genetics 2009 Jun; 84(6): 740-59. Epub 2009 Jun 4.
SigurDardo´ttir S, Helgason A, Jeffrey R. Gulcher JR, Stefansson K, Donnelly P (2000). The Mutation Rate in the Human mtDNA Control Region American Journal of Human Genetics 2000; 66: 1599–1609.

Whole-genome sequencing

Palamara PF, Franciolo LC, Wilton PR et al (2015). Leveraging distant relatedness to quantify human mutation and gene-conversion rates. American Journal of Human Genetics (article in press).
Francioli LC, Polak PP, Koren A et al (2015). Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics. Published online 18 May 2015.
Besenbacher Sm Liu S, Izarzugaza JMG (2014). Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nature Communications. Published online 19 January 2015.
Campbell CD, Eichler EE (2013). Properties and rates of germline mutations in humans. Trends in Genetics 2013; 29 (10): 575–584.
Augustine Kong, Michael L. Frigge, Gisli Masson, et al (2012). Rate of de novo mutations and the importance of father's age to disease risk. Nature 488, 471–475 (23 August 2012).